This is an article from the spring 2016 issue of LSA Magazine. Read more stories from the magazine.

Continue below to Envisioning Sight for the story of a medical researcher who uses noninvasive eye scans to look at the brain and practice preventive care, Virtual Dissection to read about how to cut open a fossil without actually cutting it open, Examining Ancient Anatomy to read about peeking inside an ancient mummy by taking it to a modern hospital, and Ocean Floor Sonar to celebrate the woman who mapped the ocean floor during a time when only men were allowed to explore it.

Envisioning Sight

We've long been told that gazing deeply into someone's eyes can reveal the secrets of their soul. But now we know that examining someone's eyes can give us a glimpse of something just as important: a person's brain.

You won’t need much equipment. A microscope and some diagnostic software will help, but the necessary instruments aren’t all that specialized—ophthalmologists can scan eyeballs using smartphones these days. Since eye exams have become such a breeze, researchers are optimistic about finding a way to easily diagnose diseases like Alzheimer’s, multiple sclerosis, and Parkinson’s with just a quick scan of a person’s baby blues or chocolate browns.

This kind of work gets Delia DeBuc (Ph.D. ’02) especially excited. Now a research associate professor in the Bascom Palmer Eye Institute at the University of Miami Miller School of Medicine, DeBuc studies how to see vision, in a sense, helping to define the connections between eyes and disease using physics and math.

DeBuc first came to Michigan from Havana, Cuba, with an undergraduate research background in neuroscience. As a Ph.D. student in LSA’s Applied Physics Program, she helped improve Lasik surgery by using novel math equations to describe the biomechanics of the cornea—the outer tissue at the front of the eye—allowing ophthalmologists to personalize surgery for diverse patients. DeBuc’s new technique modeled the shape of a cornea with more precision, letting doctors consider the quirks of each patient’s eyes, instead of a one-size-fits-all treatment.

DeBuc’s enthusiasm bubbles over when she talks about her latest project, which takes advantage of the retina as a smaller and more accessible model of the brain. The retina is an intricately complex tissue at the back of eye where the eyeball stores its rods and cones (important for seeing light and color), lots of delicate blood vessels, and nerve cells that lead directly to the brain. The retina alone contains 10 separate layers.

Image of a retina (A), with yellow lines and arrows showing where DeBuc makes her retinal scans. Diagrams represent the left and right eyes (B). DeBuc measures the thickness of retinal layers in the diagrammed sections, checking for unusual thickness and for changes in thickness over time. Image by Tátrai et al. 2012 and licensed under CC BY 4.0

DeBuc has spent lots of time customizing software that automates the measurement of those retinal layers, “so we can know their exact thickness and optical properties,” she says. “In that way, we can know which layer will be more affected by a particular disease and plan surgeries and drug treatments better.” And, in some cases, diagnose a problem before we can otherwise see it.

One example: Alzheimer’s disease symptoms appear in the retina before the disease is detectable in the brain. “Patients with Alzheimer’s often have symptoms affecting visual function, though their symptoms arise from the brain, rather than from the eyes themselves,” DeBuc says. And since the retina can be examined more easily than the brain itself, the eye can be an accessible interface for Alzheimer’s diagnosis, easy treatment, and follow-up.

“We have clinics in the community—in the neurology department at the University of Miami, with patients in Havana—and we’re collecting data right now,” DeBuc says. “We’re trying to show that we can use the eye to predict the development of Alzheimer’s disease.

“I’m really in love with it, fusing the brain and the eye. I’m finally realizing the dream I had when I came to Michigan from Havana—doing neuroscience again.”

Oh Say Can You Seed: Virtual Dissection 

“What I’d really like is a time machine, so we could go back and collect the living versions of our fossils,” says Selena Smith. A paleobotanist, Smith studies fossil plants—most often, their seeds—as a professor in LSA’s Department of Earth and Environmental Sciences and Program in the Environment. But she’s not about to sit around waiting for the perfect technology, especially because she has access to something that comes pretty close: a synchrotron.

“A synchrotron is basically like a super-high-resolution CT scanner,” Smith says. She uses the synchrotron to peer inside opaque fossil plant parts, including fruits, leaves, wood, and seeds—some as small as a few millimeters—to examine their ancient anatomy. Synchrotrons produce layers of scanned images that allow Smith to cut seeds open without actually cutting them open. Only 50 or so synchrotrons exist in the world, and Smith has traveled to facilities in Switzerland and California to use them.

In the synchrotrons, huge rings made of scaffolding, pipes, and wires form a circular path several hundred feet long, through which giant magnets force electrons to traverse that same circular path 1.5 million times per second. Researchers like Smith harness bits of the electrons’ energy by using a beamline—equipment that intercepts and guides high-velocity particles—to force that energy through a microscope. “We use a specific beamline that can get at 3-D structures, basically the same kind of X-rays you might use to look at a broken bone,” she says, although way more powerful and more precise than in a hospital. And, amazingly, Smith’s specimens can stay both fully intact and thoroughly “dissected.”

Before, Smith might have used a sharp blade to cut fossils into very thin, sequential layers, and glued those cross-sections onto microscope slides. Or she could have put a sticky plastic sheet onto a flat fossil and peeled it away to collect incredibly thin layers of the preserved material. But these days, she says, “We get museum specimens that we’re not allowed to cut or break open.”

“For some of the fossils we’ve looked at, maybe only one or a few specimens exist, so obviously the museums don’t want us cutting them,” Smith says. So she opts for the nondestructive route that synchrotrons provide, which not only takes less time than peeling by hand, but also lets her simulate the death and destruction of ancient organisms, a process known as virtual taphonomy.

Images courtesy of Selena Y. Smith

“With fossils, you can’t always control what parts you get,” Smith says. Imagine finding an ancient orange. You might find the full fruit preserved, or only the peel, or all the segments without the peel, or a single segment, or just one seed, all in various states of disintegration. It would be easy to mistake any of those hypothetical fossils as different organisms altogether. But with the 3-D data that Smith gets from synchrotrons, she can mimic the process of fossilization by digitally stripping away layers like a fruit peel, a once-fleshy segment, or the coatings of a seed.

“We had this weird fossil of a fruit with some seeds on it, and the fruit was distinctive enough that we knew there’s only one living plant with a fruit like that,” says Smith. “But the seeds in the fossil didn’t match the appearance of the living species.” She needed to dissect some modern and fossil seeds that she guessed were related and compare their internal anatomy for a positive match. “But the seeds of the living plants are something like half a millimeter in size—they’re extremely tiny, and there’s no way that you could physically go in and peel away layers.”

So Smith got beam time at a synchrotron and used high-powered X-rays to digitally strip away the coatings of some modern seeds. “We could show that, once we took away some of the outer layers of the living seeds, we found crazy shapes that looked like the fossils.”

“We’re so used to being able to go outside, and we can put a name to anything if we really want,” Smith says. “But we’ve got fossils that just don’t look like anything that’s around...So where do they fit in the tree of life?”

Bring Out Your Dead: Examining Ancient Anatomy

Mummies want to stay hidden.

But people exhume them from their tombs, of course. “In our culture in particular, because we’re fairly removed from death and dead bodies, most people don’t see dead bodies except in a fairly formal context, like at a funeral,” says Terry Wilfong, a professor of Egyptology in LSA’s Department of Near Eastern Studies and a curator at the Kelsey Museum of Archaeology. “So people are pretty curious to see mummies and what they look like inside.” One enterprising engineering student named Grant Martin (B.S.E.M.S. ’03) figured out a way to peek inside the wrappings of a child mummy in the Kelsey Museum’s collection—without unraveling a single bit of cloth.

“Once you take the bandages off, a mummy gets exposed to light, humidity, and other things that can cause deterioration, and that’s contrary to the Egyptians’ intention,” Wilfong says. “They did this so that the body would last forever.”

Martin’s plan involved taking the ancient corpse to a modern hospital. “One thing we didn’t realize,” Wilfong says, “is that it’s illegal in the state of Michigan to transport a dead body in a car unless it’s an approved vehicle.” Luckily, Martin knew an undertaker. He borrowed a funeral van, and Martin, Wilfong, and LSA professor and curator Janet Richards drove the mummy to the U-M Hospital in the dead of night, when the CT scanner at the hospital would not be occupied by patients.


CT scans of the child mummy at the U-M hospital showed unusually thick layers of linen wrapping, a wooden frame stabilizing the body, damage to the skull, and a previously unnoticed sixth finger on the mummy's left hand. Photo courtesy of Terry Wilfong

The high resolution of a CT scanner can reveal unexpected details of a mummy’s body that the wrappings conceal—much more so than the X-rays that previously had been used to examine the Kelsey Museum’s child mummy. In the 1970s, a professor in the Department of Orthodontics, James Harris, X-rayed the mummy using protocols that he developed, along with other mummies that he examined on an expedition in Egypt. Harris was interested in their teeth, which can say a lot about a mummy’s age. And while those old X-rays were hard to interpret, says Wilfong, he and Martin were optimistic that the modern CT could produce better images. They just didn’t realize how unexpected the new view would be.

“We found a gurney outside the hospital,” Wilfong says, and the crew rolled the mummy onto a freight elevator. “A lot of people at the hospital got very interested very quickly, because I guess it’s not every day that you have a 2,000-plus-year-old mummy going through your CT scanner.

“It was going back and forth through the scanner; you could see the laser shining onto it,” Wilfong continues. “We were in the technicians’ room, watching the scans as they emerged, and at one point they all started shouting, because that’s when they discovered its sixth finger.”

Photos courtesy of the Kelsey Museum of Archaeology [wrapped mummy, X-ray] Grant Martin [CT scans, 3-D model]

The polydactyl child not only had an extra finger, but also was bound to a frame of wooden stakes, probably during the mummification process. Wilfong could see that the mummy’s body was in poor condition; the child either died in an awkward position or deteriorated before the embalmers could get to the body, situations that would have called for the wooden supports. The scans also showed thick layers of linen wrapped around the remains, which explained why the small but heavy mummy took some muscle to heft out of the van and onto the gurney.

Martin combined the CT data with rapid prototyping to create a precise polymer resin model of the skull. The plastic model gave up-close, three-dimensional access to details of the mummy’s head, leading to the surprising realization that the child was two or three years old when he died—eight years younger than previously believed.

Surely more surprises lie hidden among the Kelsey Museum’s artifacts. Already, X-rays have shown that the Kelsey Museum’s dog and baboon mummies suspiciously contain human bones. Maybe one day, new technology and insights from curious students can help explain why. These questions are more than just about dead bodies, Wilfong says. Each answer unravels a bit more about the Egyptian culture and religion that’s been kept under wraps for all this time.

Depth of Knowledge: Ocean Floor Sonar

The ocean’s surface and the inaccessible depths below it hide an enormous mountain range that spans the entire globe—right there on the ocean floor. Marie Tharp (M.S. ’45) created the first detailed maps of this 40,000-mile-long mountain range, called the Mid-Oceanic Ridge, even though she wasn’t allowed to set foot on a research ship.

Before Tharp’s time, the conventional way to explore the ocean’s depths involved attaching a heavy weight to a rope, tossing it overboard, waiting for it to thunk on the sea floor (hopefully without first giving a porpoise a concussion), and measuring the length of wet rope as the crew yanked it back to the surface. Another method involved dropping dynamite into the drink and recording the time it took to hear the explosion, assuming the dynamite didn’t explode on the ship’s deck.

But in the 1940s, researchers were developing technology that could measure the bumps of the ocean floor easily and accurately—the beginnings of sonar. At around that time, Tharp scored a job in the very lab at Columbia University where those innovations were being designed and deployed.

Marie Tharp essentially was assigned the tasks of a human calculator when she first began working at a geology lab at Columbia University. Later, she drafted copies of simple maps and diagrams. Eventually, Tharp created the first original maps that detailed the contours of the ocean floor. Photo courtesy of the Marie Tharp Estate and the Lamont-Doherty Earth Observatory

Born in Ypsilanti, Tharp grew up all over the country, tagging along with her father on soil-surveying expeditions for the U.S. Department of Agriculture, a highly unusual pastime for a young girl in the 1920s. She earned an undergraduate degree in Ohio with two majors and four minors. In 1943, she enrolled at Michigan for a master’s in geology—an easier prospect when most male students were off at war—where she did fieldwork at U-M’s Camp Davis in Wyoming and wrote a thesis about the geology of the Detroit River. She earned yet another degree in math while working full time for a petroleum company in Oklahoma. And then she wound up in New York.

Women on ships were considered bad luck, so Tharp had no hopes of collecting her own data. Instead, Bruce Heezen, a male graduate student who was younger, less educated, and less experienced than she, brought back data from his own research expeditions at sea. Heezen worked as Tharp’s direct supervisor and, eventually, her close research partner. Through Heezen and the Columbia lab, Tharp had access to reams of sonar data gathered by vessels plowing through the Atlantic Ocean between western Africa and the eastern United States, which she translated into the contours of the ocean floor. Those sonar data, though, only traced the narrow passages along the routes of six separate ships that traveled many miles away from one another. So Tharp applied her expertise to infer the geological features in the blank spaces between the ships.

While Tharp drew her maps by hand—a process that took months—another member of the lab sat at an adjacent drafting table, plotting the locations of tens of thousands of earthquakes that had been recorded in the open ocean. The aim was to find a safe spot to install transatlantic telegraph cables. Amid the gigantic mountains of the Mid-Oceanic Ridge that Tharp outlined on her maps, she soon noticed that a deep notch interrupted the series of peaks. That notch—an enormous valley, it looked like, wider than the Grand Canyon—aligned at about the same spot in all the ships’ paths. Most surprising of all, the earthquake epicenters plotted at the table next to Tharp’s lined up perfectly with the valley that Tharp had drawn.

When Jacques Cousteau heard about the unlikely valley, he dragged a camera behind his ship to investigate. Cousteau was so shocked to find that the valley actually existed, he turned the boat around and filmed it again. Photo courtesy of Library of Congress, Geography and Map Division

This discovery blew everyone away, because the notch in Tharp’s map implied that the roiling disturbances of volcanoes, accompanied by molten rock pushing up through the sea floor, caused earthquakes that forced the mountain range’s peaks ever higher through unseen layers of the ocean’s abyss. No scientist wanted to admit that the Earth’s crust was in turmoil at invisible depths. If they did, then experts would have to acknowledge that the seemingly insensible idea of continental drift—the infinitesimally slow movement of the continents relative to one another—was true. Years went by as Tharp continued to map essentially the entire ocean floor until the skeptical scientific community acknowledged the great valley she’d spotted in the sonar data and its geological implications.

Tharp’s painstakingly drawn maps, her persistence, and her willingness to challenge social and scientic norms changed how we see the ocean floor. Her discoveries led to our current understanding of plate tectonics and the solid but surreal evidence that the continents are moving beneath our feet.

Throughout her life, Tharp worked toward making her maps accessible to the general public, convinced that more than just a narrow demographic of researchers should be able to see and uncover Earth’s secrets. Tharp’s maps were first published in colorful detail by National Geographic in 1977. They were exhibited at the Library of Congress, alongside maps drawn by George Washington and pages from Lewis and Clark’s journals. Google Earth overlaid Tharp’s maps onto its digital ocean.

Through her work, Tharp saw not only what remained invisible on the ocean floor, but also the hidden possibilities for what she as a woman could do in her male-dominated world. For Tharp, challenging social barriers imposed on her gender was no less a feat than diving to great depths to map the ocean floor without even getting near the water—and she did both.